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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgttttgttaacgcttcttttttgtacacagttatgccaattttgatttcttgttttaattatgtgttgtgtggcttggttttgtgtttcag

Basic information

species Glycine max
transcript GLYMA16G32990.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 2
CTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgttttgttaacgcttcttttttgtacacagttat-gccaattttgatttcttgttttaattatgtgttgtgtggcttggttttgtgtttcag
 | ||  | || ||||| || ||  |||||||| | ||||||||||| |||||||||||||| || || ||  |||| || ||||| || || ||||||||||   ||   ||||   |      ||     ||| | | ||  ||    | ||  ||  | ||  || |         |||  |  |     ||||
ATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAATTCAGGCCTACGTCTTTGATGgtaaaatt--attaatattgaacaatt-----cagctgttgctcatagcaaattactgactcaaaaatcta----accactttttccttgaaatcag

upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 1
CTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgttttgttaacg---cttcttttttgtacacag-ttatgccaattttgatttcttgttttaattatgtgttgtgtggcttggttttgtgtttcag
 | ||  | || || ||||| ||  | |||||||| || ||||||||||||||||||||||| || || ||| |||| |||||||| || || |||||||||    | ||   | ||    |||||  || | ||| | |||||   | | | |  |     || |||| |    | || |   | |             
ATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAATCCAGGCCTACGTCTTTGATGgtgaattattagcaccgagctttcttggttttgcacggcttatg---agtataacctgacacttgaatttt----tatgagaaatag-------------

upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G51570.1 (Arabidopsis thaliana), 5'ss of exon 2
CTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgttttg------ttaacgcttcttttttgtacacagttatgccaattttgatttcttgttttaattatgtgttgtgtggcttggttttgtgtttcag
 | ||||||||||| || || ||  | || |  |  ||||||||||| || |||||| | ||||||||| | ||||||||||| |||||||| |||||||||| | ||||        |   | |  |||||  | |   |||     ||  |   |||    | || |||   | |||| ||  |   |||||  |   ||
GTTTGTTCGATTCAGTATCGTGTAGTGAAAGCTAGTGCTGATGATGCGTTTTATGAGCTTCAAAACCCTAAAGAGCAGATCCAAGCTTATGTCTTTGATGgtaatttttttgcttctctgttgatgttttttgtttctttgtttgaagaagctctgttttgattcttgatttgttcttgtatgtttgttttttgaatcatag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|298190343|gb|HO032464.1|HO032464
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|254327495|gb|GR837050.1|GR837050
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|213603197|gb|DB960460.1|DB960460
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|254346709|gb|GR856431.1|GR856431
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|192328203|gb|FK022882.1|FK022882
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|298179574|gb|HO028045.1|HO028045
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|51345167|gb|CO985900.1|CO985900
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|209701321|gb|BW655916.1|BW655916
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|298184948|gb|HO030161.1|HO030161
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|298164789|gb|HO010786.1|HO010786
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|16347781|gb|BI973376.1|BI973376
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|298197264|gb|HO042007.1|HO042007
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
EST: gi|120530546|gb|EH258679.1|EH258679
EST:     CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATG                         TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA
genomic: CTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgtttt ... tgtgtttcagTGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGATCCAGGCTTATGTTTTTGATGgtagtgttttgttaacgcttcttttttgtacacagttatgccaattttgatttcttgttttaattatgtgttgtgtggcttggttttgtgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT